This repository contains the pipeline for quality control of human genome/exome cohorts

The code is written by members of Wellcome Sanger HGI group (https://www.sanger.ac.uk/group/human-genetics-informatics-hgi/) based on the gnomAD QC v3 pipeline by Broad institute (https://github.com/broadinstitute/gnomad_qc/tree/main/gnomad_qc/v3).

The code is designed to run standalone or on the SPARK cluster with the Hail library installed.

The high-level description of the QC process is available in a separate document: WxS-QC concepts.

Detailed howto for the QC process is here: WcS-QC howto. For this howto we used an open example dataset, described here

When working on an analysis branch, you can retrieve the latest changes from the main branch by running:

make update

This will fetch the latest changes from the main branch and rebase your current branch onto it. If there are any unstaged changes in the branch, you will be asked to commit or stash them first.

For improving the pipeline and developing new functionality, the Developer's howto is available.